Isolation of bacteriophage host strains of Bacteroides species suitable for tracking sources of animal faecal pollution in water

Abstract

Microbial source tracking (MST) methods allow the identification of specific faecal sources. The aim is to detect the sources of faecal pollution in a water body to allow targeted, efficient and cost-effective remediation efforts in the catchment. Bacteriophages infecting selected host strains of Bacteroides species are used as markers to track faecal contaminants in water. By using a suitable Bacteroides host from a given faecal origin, it is possible to specifically detect bacteriophages of this faecal origin. It can thus be used to detect specific phages of Bacteroides for MST. With this objective, we isolated several Bacteroides strains from pig, cow and poultry faeces by applying a previously optimized methodology used to isolate the host strains from humans. The isolated strains belonged to Bacteroides fragilis and Bacteroides thetaiotaomicron. These strains, like most Bacteroides species, detected phages of the Siphoviridae morphology. Using the newly isolated host strains for phage enumeration in a range of samples, we showed that these detect phages in faecal sources that coincide with their own origin (70-100% of the samples), and show no detection or very low percentages of detection of phages from other animal origins (from 0 to 20% of the samples). Only strains isolated from pig wastewater detected phages in 50% of human sewage samples. Nevertheless, those strains detecting phages from faecal origins other than their own detected fewer phages (2-3 log₁₀ pfu·100 ml⁻¹) than the phages detected by the specific strain of the same origin. On the basis of our results, we propose that faecal source tracking with phages infecting specific Bacteroides host strains is a useful method for MST. In addition, the method presented here is feasible in laboratories equipped with only basic microbiological equipment, it is more rapid and cost-effective than other procedures and it does not require highly qualified staff.

Comparative (Meta)genomic Analysis and Ecological Profiling of Human Gut-Specific Bacteriophage φB124-14

“…Faecal contamination of surface waters poses a major risk to public health, and bacteriophages specific to human faecal indicator bacteria (and the human gut microbiome) have already been successfully employed as water quality indicators that can specifically identify pollution originating from human sources [20]–[22], [25], [26]. Bacteriophage offer numerous advantages in these applications and are not only thought to persist longer in the environment than host bacteria but can often be found in higher numbers making them a more sensitive source tracking tool [22]. In particular, the development of rapid and sensitive culture-independent methods for detection of human faecal indicator phage, directly in environmental samples, offers significant advantages over classic culture-based approaches, and there is presently much interest in developing and implementing such strategies [27].…”

New Molecular Quantitative PCR Assay for Detection of Host-Specific Bifidobacteriaceae Suitable for Microbial Source Tracking

“…They include antibiotic-resistant enterococcus phenotypes (18), bacteriophages of Bacteroides spp. (17,23,38), F-RNA bacteriophage subgroups (21), Rhodococcus coprophilus (41), Bacteroides group (8, 39), Bifidobacterium spp. (3,6,7,11,25,31), and biochemical fingerprinting of bacterial populations (32).…”

The capability of non-native strains of Bacteroides bacteria to detect bacteriophages as faecal indicators in a tropical area

“…A previous study in a river with an intermediate contamination level, which receives inputs from industrial areas and the secondary effluents of municipal wastewater treatment plants, showed a median number of 7·9 PFU 100 ml −1 and a maximum value of 120 PFU 100 ml −1 with 85% positive detection for RYC2056PH (Gómez‐Doñate et al . ). Another study of rivers from Europe and South America revealed that 70% of the samples tested contained RYC2056PH, and the averaged concentrations ranged from below 10 to above 100 PFU 100 ml −1 when stratifying the data based on faecal coliforms levels (Lucena et al .…”

“…This group of phages has been found in faecally polluted water bodies, including river water (Araujo et al 1997;Dur an et al 2002), river sediment (Tartera and Jofre 1987), seawater (Contreras-Coll et al 2002;Moc e-Llivina et al 2005) and groundwater . To date, studies of indigenous Bacteroides phages have been conducted in a number of geographical regions, mostly in temperate climates, including those in Mediterranean and European countries (Tartera and Jofre 1987;Araujo et al 1997;Contreras-Coll et al 2002;Dur an et al 2002;Pay an et al 2005;Blanch et al 2006;G omez-Doñate et al 2011;Wicki et al 2011;Muniesa et al 2012), the continental USA (Kator and Rhodes 1992), South Africa (Grabow et al 1995), Hawaii (Vijayavel et al 2010) and South America (Lucena et al 2003). Because different climates could affect microbial behaviours and environmental factors, Bacteroides bacteriophages require further investigations in a wider set of geographical areas, including tropical countries, to ensure their worldwide use.…”

“…Bacteriophage RYC2056PH has been reported to be found in high numbers in a wide range of geographical areas in European and Mediterranean areas but did not differentiate between human-and animal-specific phages. This phage strain could therefore be used to indicate faecal pollution without specifying human or animal sources (Pay an et al 2005;G omez-Doñate et al 2011;Jofre et al 2014). Therefore, this type of phages was chosen for studying in Thailand to compare its abundance and relative specificity.…”